The original line was commissioned in September 1878, and opened on 21 May 1879. It connected Queenscliff with South Geelong station, the terminus of the Geelong line, and the junction of the Warrnambool line. It was acknowledged at the time that although passenger traffic alone might not justify a railway line, military traffic from both the port and Fort Queenscliff—a key defence installation—would warrant its construction. It initially carried passenger, goods and military traffic, and continued to do so for several decades.

In the first few months of operation, it carried only one service per day, but at its peak, in January 1885, four trains per day ran in each direction, enabling the line to be used by commuters. However, this was decreased to three not long after, and was cut back to two trains a day in 1910. Traffic on the line continued to fall over the next twenty years, and in 1931, passenger services were dropped completely—apart from the occasional Sunday excursion train. Goods services continued to run, although they were cut to back at first to twice-weekly, and then weekly operation.

The line saw a revival during World War II, carrying mines from the Swan Island military base, but returned to pre-war levels afterwards. After the war, services became less frequent, with passenger services dropped altogether, apart from occasional special trains, and with goods services cut back to one a fortnight. The line was closed on 6 November 1976.